fc-cache and fc-list _ought_ to work; their man pages may be missing, though,
so you'll have to dig them out of the package. I've found that I sometimes need
to clear the caches and re-run fc-cache; very occasionally I've added a fonts.dir
file by hand. (mkfontdir creates a list of fonts in a directory, but doesn't add an
empty fonts.dir) The best way of listing font paths seems to be "xset -q"

Ok, a bit more digging and the machine which accesses a lot of fonts seems to
still have an xorg.conf. The one without xorg.conf just has the standard path
(I don't know where it's set). It looks as if "xset fp+ ..." and "xset fp rehash"
is the standard way to go.

There's no universal fonts handling. Well, most of modern applications rely on fontconfig. For those applications nothing special has to be done, since the font by default is installed into directory known to fontconfig and all necessary actions are taken to add new font to the list.

But I guess there are still applications out there that don't know how to use fontconfig. Those may still rely on fonts being in directories known to xorg. Personally, I haven't used such applications recently, so I can't provide examples.

Like many others, I do use Terminus and proggy fonts and they show up without any tweaking in gvim and xfce-terminal. They are not visible in xfontsel, which does not bother me. Again, I don't have any application that would pick-up fonts using old way.

So, if some application does not see these fonts, then you should provide information about that application, then someone may be able to give more specific advice. Without those details, I can only say, that fontconfig may exclude bitmap fonts from the list. There's configuration file that does this. Check output of eselect fontconfig list and search for 70-no-bitmaps.conf

Well, vim itself does not use any fonts. It relies on the terminal to handle this stuff. Only gvim is capable of handling fonts, and when it is compiled with gtk, then it can use fonts provided by the fontconfig. If another toolkit is used, then you may have to provide fonts using old way.

I don't know much about rxvt-unicode (I prefer xfce-terminal for unicode stuff). But I'm pretty sure, that xterm does not know how to use fontconfig. It expects font names like -misc-fixed-medium-r-semicondensed-*-13-*-*-*-*-*-*-* which comes from old system and is not supported by fontconfig. So, if you want to use Terminus with this application then you have to add the directory /usr/share/fonts/terminus/ to the FontPath. By default it is not added.

Checking the configuration for i3, it seems, that it also does not use fontconfig for obtaining fonts. It expects the same font names as xterm. So, I guess the same stuff applies to i3 as to xterm.

So i guess if i want to use that sort of fonts (not Xft etc.) then i have to stick with xorg.conf/xset :/

I would say "If you want to use that sort of applications, then you have to stick with xorg.conf". No, I don't have anything against the applications, just want to make clear, that this sort of fonts is perfectly usable without xorg.conf